A method for controlling intake and exhaust valves of an engine includes: Controlling opening and closing timings of the intake and exhaust valves by an intake continuous variable valve timing (CVVT) device and an exhaust CVVT devices; determining, by a controller, target intake and exhaust opening durations of the intake and exhaust valves, and target opening and closing timings of the valves based on an engine load and an engine speed; modifying current intake and exhaust opening durations based on the target opening durations via an intake continuous variable valve duration (CVVD) device and an exhaust CVVD device; adjusting opening or closing timings of the valves to the target opening or closing timings of the valves while maintaining the modified opening durations of the valves.